Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

Abstract

BACKGROUND:

Recent studies suggest that the regulation of longevity may be partially conserved in many eukaryotes ranging from yeast to mammals. The three yeast mutants sch9Delta, ras2Delta, tor1Delta show extended chronological life span up to three folds. Our aim is to dissect the mechanisms that lead to the yeast life span extension.

METHODOLOGY/PRINCIPAL FINDINGS:

We obtain gene expression profiles of sch9Delta, ras2Delta, tor1Delta as well as that for a wild type at day 2.5 in SDC medium using Affymetrix Yeast2.0 arrays. To accurately estimate the expression differentiation between the wild type and the long-lived mutants, we use sub-array normalization followed by a variant of the median-polishing summarization. The results are validated by the probe sets of S. pombe on the same chips. To translate the differentiation into changes of biological activities, we make statistical inference by integrating the expression profiles with biological gene subsets defined by Gene Ontology, KEGG pathways, and cellular localization of proteins. Other than subset-versus-other comparisons, we also make local comparisons between two directly-related gene subsets such as cytosolic and mitochondrial ribosomes. Our consensus is obtained by cross-examination of these inferences. The significant and systematic differentiation in the three long-lived strains includes: lower transcriptional activities; down-regulation of TCA cycle and oxidative phosphorylation versus up-regulation of the KEGG pathway Glycolysis/Gluconeogenesis; the overall reduction of mitochondrial activities. We also report some different expression patterns such as reduction of the activities relating to mitosis in ras2Delta.

CONCLUSIONS/SIGNIFICANCE:

The modification of energy pathways and modification of compartment activities such as down-regulation of mitochondrial ribosome proteins versus up-regulation of cytosolic ribosome proteins are directly associated with the life span extension in yeast. The results provide a new and systematic S. cerevisiae version of the free radical theory from the perspective of functional genomics.

After the preprocessing of the microarray data for the long-lived cells versus the wild type, we translate the differentiation into changes of biological activities by consensus and local inference using three kinds of biological instruments: Gene Ontology (GO), KEGG pathways, and cellular localization of proteins.

The estimates of the normalization scale in each subarray are shown by their spatial locations. We normalize each of the three target (sch9 mutant) arrays versus each of the three reference (wild type) arrays, and total nine spatial patterns are shown. Each row corresponds to a reference and each column corresponds to a target.

In the M-A plots, the x, y coordinate value of a dot respectively show the average and difference of a gene expression between the wild type and a mutant. The differentiation for most probe sets of S. pombe are around zero as expected. Black: S. cerevisiae; Magenta: S. pombe. Top: sch9 mutant; Middle: ras2 mutant; Bottom: tor1 mutant. Two horizontal lines at ±0.15 are also plotted.

Top panel: The box plots of the log-ratios of gene expressions for Glycolysis/Gluconeogenesis, TCA, and Oxidative phosphorylation in the long-lived mutants with respect to wild type; bottom: statistical significances of the above comparisons using the Wilcoxon rank test.

The box plots of expression log-ratios for the cytosolic and mitochondrial ribosome proteins in the long-lived mutants with respect to wild type. We also compare the expression differentiation by the Wilcoxon rank test and all three p-values are 0.00.